Diversity of soil Archaea in boreal forest before, and after clear-cuttingand prescribed burning

Genetic diversity of forest soil Archaea was measured by extraction of tota l DNA from forest soil samples followed by polymerase chain reaction-restri ction fragment length polymorphism (PCR-RFLP), Southern blot hybridization and phylogenetic analysis of archaeal 16S rDNA. Soil samples from boreal fo rest treated with two regeneration practices were studied: clear-cutting (A ) and clear-cutting followed by prescribed burning (B) 2 years later. The s amples collected 1 year after the prescribed burning included a control soi l (C) from an untreated standing forest. The PCR products from the three di fferent soil samples were cloned and analyzed by RFLP. Soil samples A, B an d C gave eight, nine and six different restriction profiles, respectively. New electrophoreses were run with clones of different digestion patterns, f ollowed by Southern blotting and DNA hybridization with two different Crena rchaeota-specific oligonucleotide probes. Selected clones were sequenced an d phylogenetically characterized. It was discovered that the clones from so ils A and B are similar and differ from the clones isolated from the contro l soil C. Both the RFLP-hybridization study of the clones and phylogenetic analysis of selected sequences from all three types of soil supported the d ivision of the new Crenarchaeota into two subgroups. It is shown that the R FLP-hybridization technique can be successfully used for preliminary evalua tion of clone diversity in the rDNA library. (C) 1999 Federation of Europea n Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.